Biochemistry PDF - Protein Structure

17 18 Noor Aldeen Alfaouri Besan Al-ameir & Hala Abu-Dyouk Lujain WaqarAl-awamleh Alfaqeer Dr.Nafez Abutarboush 1  Protein In previous lecture we talked about protein structure, levels o...

17 18 Noor Aldeen Alfaouri Besan Al-ameir & Hala Abu-Dyouk Lujain WaqarAl-awamleh Alfaqeer Dr.Nafez Abutarboush 1  Protein In previous lecture we talked about protein structure, levels of structure which mean how do you synthetizes your protein? How do you build up your protein? What are the steps every protein should take to build up? Also, we talked about the primary structure of protein and how structure is related to function by example and how the defect in this structure affects the rest, as we have seen in some diseases. Now we will start: Secondary structure Localized (close) area of protein where they warp around each other. Why does that happen? because the resulting bond formed by warping are more stable The protein is folding to reduce the energy and make high stability by arrangement polar and non-polar amino acid What is it? How is it caused? ▪ The two bonds within each amino acid residue freely rotate – the bond between the a-carbon and the amino nitrogen – the bond between the a-carbon and the carboxyl carbon ▪ A hydrogen-bonded, local arrangement of the backbone of a polypeptide chain Polypeptide chains can fold into regular structures such as: ▪ Alpha helix ▪ Beta-pleated sheet ▪ Turns ▪ Loops 1 The alpha helix: Helical shape it is specific Secondary protein structure, it has own special characteristic Which mean not all helical structure is alpha helix. 3.6 amino acids per turn every 18 amino acids have 5 bonds The pitch of the helix (the linear distance between corresponding. points on successive turns) are5.4 Å (10^-10) It is very stable! Avoiding steric hindrance the direction of R group in amino acids are outside the helix. The H bond between the H in the amino group (amino acid number 1) & O in the carboxylic group (amino acid number 4) Amino acids NOT found in α-helix. Glycine: too small (always breaker to a helix) Proline – No rotation around N-Ca bond – No hydrogen bonding of a-amino group Close proximity of a pair of charged amino acids with similar charges Amino acids with branches at the β-carbon atom (valine, threonine, and isoleucine). β pleated sheet (β sheet) zig-zag ▪ They are composed of two or more straight chains (β strands) that are hydrogen bonded side by side (typically 4 or 5) ▪ Optimal hydrogen bonding occurs when the sheet is bent (pleated) to form β-pleated sheets. 2 ▪ β sheets can form between many strands, typically 4 or 5 but as many as 10 or more. ▪ Such β sheets can be purely antiparallel, purely parallel, or mixed. loop or tur ‫ يرتبطوا عن طريق‬amino acids ‫ممكن‬ Effect of amino acids ▪ Valine, threonine, and Isoleucine with branched R groups at β-carbon and the large aromatic amino acids (phenylalanine, tryptophan, and tyrosine) tend to be present in β-sheets. The branches in amino acids do not disrupt the B SHEET ▪ Proline and glycine tend to disrupt β strands The H bond in alpha helix with the long axis while H bond in the B SHEET is perpendicular to it. β-turns ▪ Turns are compact, U-shaped secondary Structures (connect B SHEET together ) ▪ They are also known as β turn or hairpin bend ▪ What are they used for? How are they stabilized? ▪ Glycine (too small) and proline(it cause this sharp turns ) are commonly present in turn Loops and coils ▪ Loops are a diverse class of secondary structures in proteins with irregular geometry and that connect the main secondary structures. ▪ They are found on surface of molecule (and contain polar residues) and provide flexibility to proteins. ▪ Amino acids in loops are often not conserved. Mostly loops have more than 4 amino acid 3 EXTRA information about this statement by chatGBT (Read only ) Ligands& antigen ‫يوجدفي مكان ارتباط‬ The presence of loops in ligands and antigens plays a crucial role in their interactions and functionality. These loops provide structural flexibility and specificity, which are essential for various biological processes. Here are the key benefits: 1. Improved Flexibility and Adaptability: Loops add flexibility to the molecule, allowing it to adapt to the surface of the interacting partner. This enhances the binding compatibility between the ligand and antigen. Flexibility enables conformational matching, ensuring a more precise fit during interactions. 2. Strengthened Interaction with the Binding Site: Loops often contain critical residues that directly interact with the active or binding site, increasing the binding affinity and specificity. In antibodies, the loops in CDRs (Complementarity-Determining Regions) play a key role in recognizing specific antigens. 3. Increased Binding Surface Complexity: Loops introduce structural diversity, creating a more complex and versatile binding surface. This enables ligands or antigens to interact effectively with various proteins or receptors. 4. Enhanced Specificity in Recognition: In antigens, loops often form epitopes, which are recognized by antibodies or immune receptors. The structural variability of loops allows antigens to present unique binding sites. In ligands, loops facilitate precise positioning for interaction with receptors, ensuring specific recognition and binding. 5. Structural Stability: Despite being flexible, loops can contribute to the overall structural stability of the molecule through interactions like hydrogen bonds or other stabilizing forces. 6. Facilitating Dynamic Interactions: Loops enable structural adjustments during interactions, allowing ligands or antigens to adapt to environmental changes, such as pH variations or binding-induced conformational changes. Examples: Antibodies: Loops in variable regions, such as CDR1, CDR2, and CDR3, allow antibodies to recognize diverse antigens with high specificity. Receptors and Ligands: Loops in receptors or ligands are crucial for forming strong and specific interactions, such as hormone-receptor binding 4 Tertiary structure What is tertiary structure? 3D arragment of protien (anybonds ‫(ممكن يكون موجد فيها‬ The overall conformation of apolypeptide chain. The three-dimensional arrangement of all the amino acids residues. The spatial arrangement of amino acid residues that are far apart in the sequence. Myoglpain have tertiary structure. The bonds and interactions that maintain the stability of the tertiary structure of proteins: 1. (Covalent Bonds): Disulfide Bonds: Formed between the sulfur atoms in the thiol groups (-SH) of two cysteine amino acids. These bonds are very strong and contribute significantly to the stabilization of the tertiary structure. 2. (Non-Covalent Bonds): Hydrogen Bonds: Occur between hydrogen atoms bonded to electronegative atoms (like oxygen or nitrogen) and other electronegative atoms within the protein. These bonds help stabilize the structure. Hydrophobic Interactions: Nonpolar side chains of amino acids cluster together inside the protein, away from water, contributing to the folding of the protein. Van der Waals Interactions: Weak forces between closely positioned atoms or molecules that contribute to the overall stability of the structure. Electrostatic Interactions (Ionic Bonds): Bonds formed between amino acids with positive and negative charges (e.g., lysine and glutamate). 3. Environmental Effects: Conditions such as pH, temperature, and ion concentration can enhance or reduce the stability of these bonds, thereby influencing the tertiary structure. 5 Non-covalent interactions: ▪ Hydrogen bonds: 1. within and between polypeptide chains; 2. with the aqueous medium ▪ Charge-charge interactions (salt bridges, ionic): oppositely charged R-groups ▪ Charge-dipole interactions: charged R groups with the partial charges of water Hydrophobic interactions :( not actual interaction ) the most important intraction that Determin the shape of protein ▪ A system is more thermodynamically (energetically) stable when hydrophobic groups are clustered together(make glopular shape ) rather than extended into the aqueous surroundings. Can polar amino acids be found in the anterior ? ….yes ▪ Polar amino acids can be found in the interior of proteins ▪ In this case, they form hydrogen bonds to other amino acids or to the polypeptide backbone ▪ They play important roles in the function of the protein 6 Stabilizing factors ▪ There are two forces that do not determine the 3D-structure of proteins, but stabilize these structures: – Disulfide bonds – Metal ions ▪ Covalent ▪ Salt bridges Myoglopin have histedene& hem Quaternary structure What is it? Proteins are composed of more than one polypeptide chain. – They are oligomeric proteins (oligo = a few or small or short; mer = part or unit) The spatial arrangement of subunits and the nature of their interactions. Proteins made of – One subunit = monomer Each polypeptide chain is called a – Two subunits: dimer subunit The simplest: a homodimer Oligomeric proteins are made of multiple polypeptides that are – Three subunits: trimer identical homooligomers (homo = – Four subunit: tetramer same), or different heterooligomers (hetero = different) 7 How are the subunits connected? Sometimes subunits are disulfide-bonded together, other times, noncovalent bonds stabilize interactions between subunits. Properties of Proteins: Protein Hydrolysis 8 Denaturation ▪ Solubility ▪ Heat ▪ Mechanical ▪ Extremes of pH : ionic intraction ‫بتأثر على‬ ▪ Organic compounds: acetone, ethanol, bacterial proteins ▪ Detergents (Triton X-100 (nonionic, uncharged) and sodium dodecyl sulfate (SDS, anionic, charged)) disrupt the hydrophobic forces. – SDS also disrupt electrostatic interactions. ▪ Urea and guanidine hydrochloride disrupt hydrogen bonding and hydrophobic interactions. ▪ Reducing agents such as β-mercaptoethanol (βME) and dithiothreitol (DTT)Both reduce disulfide bonds ‫ الن الروابط غير القطبية ستواجه الماء‬function ‫رح يأثر على ال‬ Denaturation and Its Relation to Eggs: When an egg is cooked, the heat causes the proteins in the egg white (primarily albumin) and yolk to denature. Before cooking: The proteins in the egg are in their native folded state, dissolved in water, and appear transparent. ‫ والبيروكسيدات تعمل على قتل الكائنات الحية‬،‫ اليود‬،‫ الكلور‬،‫المعقمات مثل الكحول‬ During cooking: Heat breaks the weak non- ‫ عملية التغير في‬.‫ وذلك من خالل تأثيرها المباشر على البروتينات في الخاليا‬،‫الدقيقة‬ covalent bonds (hydrogen bonds, ‫( طبيعة البروتين‬Denaturation) ‫هي أحد أهم اآلليات التي تستخدمها المعقمات‬ hydrophobic interactions, etc.) that maintain ‫لتعطيل وظائف البروتينات الحيوية داخل الكائنات المسببة لألمراض‬ the protein’s tertiary and secondary structures. This allows the protein chains to unfold and aggregate, forming a solid, opaque structure. ‫تمت كتابة هذا الشيت صدقة جارية عن روح والدة زميلنا عمرو رائد من دفعة تيجان‬ ‫دعواتكم لها بالرحمة والمغفرة‬ 9